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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sesame_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.24.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘sesame’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
testEnrichmentGene            67.089  4.353  74.115
imputeBetasByGenomicNeighbors 60.638  1.600  63.324
inferSex                      38.193  1.307  39.798
sesameQC_calcStats            34.736  2.038  37.361
KYCG_plotMeta                 32.210  1.177  34.471
compareMouseStrainReference   30.680  0.578  32.992
sesameQC_plotHeatSNPs         29.091  1.507  31.154
KYCG_plotEnrichAll            28.713  1.768  31.034
compareReference              27.870  0.980  31.273
imputeBetas                   26.435  1.850  28.737
ELBAR                         22.924  3.421  26.859
diffRefSet                    23.988  1.028  25.402
KYCG_annoProbes               23.255  1.164  25.471
matchDesign                   21.885  1.120  23.280
inferSpecies                  20.897  0.973  22.179
getRefSet                     18.817  0.736  19.711
sesameQC_plotBar              19.059  0.485  19.861
sesameQC_plotBetaByDesign     17.348  1.549  19.075
DML                           17.064  1.678  19.598
KYCG_plotMetaEnrichment       17.782  0.729  18.819
visualizeGene                 17.395  0.841  18.542
testEnrichmentSEA             15.982  1.364  17.562
KYCG_buildGeneDBs             16.094  0.637  17.342
sdf_read_table                15.133  0.663  16.373
DMR                           15.040  0.377  15.600
deidentify                    14.203  0.538  15.049
inferStrain                   12.920  0.695  13.835
inferTissue                   11.085  1.453  12.743
reIdentify                    11.990  0.313  12.442
dbStats                       10.702  0.910  11.983
estimateLeukocyte             10.397  0.727  11.334
getMask                       10.294  0.812  11.547
openSesame                     9.357  0.907  10.395
KYCG_plotSetEnrichment         9.581  0.681  10.365
dyeBiasNL                      9.314  0.538   9.918
createUCSCtrack                9.334  0.425   9.893
dyeBiasCorrMostBalanced        9.295  0.361   9.779
testEnrichment                 8.480  1.014  10.040
probeSuccessRate               8.489  0.656   9.287
bisConversionControl           7.396  0.353   7.821
parseGEOsignalMU               5.606  1.184   6.903
noMasked                       6.068  0.678   6.897
prepSesame                     6.306  0.357   6.820
scrubSoft                      5.150  1.239   6.530
updateSigDF                    5.327  0.482   5.849
sesameQC_rankStats             5.394  0.368   5.987
sdf_write_table                5.158  0.308   5.722
print.DMLSummary               4.459  0.889   5.424
checkLevels                    4.766  0.500   5.339
summaryExtractTest             4.030  1.080   5.350
detectionPnegEcdf              4.806  0.207   5.127
KYCG_plotWaterfall             4.732  0.272   5.044
totalIntensities               4.660  0.324   5.043
dyeBiasCorr                    4.602  0.339   5.079
KYCG_getDBs                    4.552  0.379   5.041
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sesame
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘sesame’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sesame)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(sesame)
Loading required package: sesameData
Loading required package: ExperimentHub
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading sesameData.

----------------------------------------------------------
| SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
| --------------------------------------------------------
| Please cache auxiliary data by "sesameDataCache()".
| This needs to be done only once per SeSAMe installation.
----------------------------------------------------------

> 
> test_check("sesame")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
 35.142   2.775  38.600